Tag: protein

Ribosome profiling surveys the complement of mRNA undergoing active translation

December 25, 2020

Differential gene expression is one highly coordinated ancestral mechanism that allow cells to respond to new environmental and nutritional status while conserving cellular resources for use when necessary. Such an approach enables cells to only express the genes needed at a particular moment; thereby, reducing wastage of cellular energy and building blocks that would be … More Ribosome profiling surveys the complement of mRNA undergoing active translation

Plunge-freezing enables cryo-EM to analyse proteins in the frozen state

November 13, 2020

Cryo-electron microscopy (cryo-EM) uses an electron beam to generate electron scattering and diffraction information when the electrons interact with a molecule; thereby, helping to generate an image of the molecule. However, the method would not work if the proteins are able to move freely. Thus, a method for fixing the protein molecule in space and … More Plunge-freezing enables cryo-EM to analyse proteins in the frozen state

Translation rate could be inferred from Ribo-seq data

August 30, 2019

Methods to characterise translation of proteins would provide a wealth of data useful for understanding gene expression and how different environmental factors affect protein abundance in cells. However, despite the availability of quantitative proteomics approaches, there is a relative dearth of methods able to obtain more insights into the cellular dynamics of gene expression and … More Translation rate could be inferred from Ribo-seq data

Different proteins could annotate a single mass peak of a mass spectrum

May 24, 2018

Functional annotation of mass spectrum of bacterial cells obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) generates the biological meaning that underpins the use of mass spectrometry for microbial identification. However, different proteins could have the same mass/charge ratio and thus able to annotate the same mass peak in a mass spectrum. Such … More Different proteins could annotate a single mass peak of a mass spectrum

Utility of rescue experiments in biology

February 9, 2018

Loss of function assays are common in biology for understanding the function associated with a protein or gene. Typically, targeted mutagenesis is used for creating a specific gene or protein mutant, that due to loss of critical sequence information, result in a loss of function. Thus, the function lost can be associated with the gene … More Utility of rescue experiments in biology

Phylogenetic trees track the evolutionary relatedness of genes and proteins

December 22, 2017

The tree of life is currently defined by a phylogenetic analysis of the 16S rRNA gene, which harbours deep evolutionary information on the development of various species on Earth. Specifically, it is highly conserved across species, and yet possesses sufficient variability for individual species to be identified by differential sequence at the gene level. Thus, … More Phylogenetic trees track the evolutionary relatedness of genes and proteins

Computer modelling for fitting possible structures to diffraction data

November 28, 2017

Modern structural biology is a combination of diffraction experiments using X-rays or electron, and computer simulation for fitting possible structures to the diffraction data.   Specifically, after protein crystallization and determination of structure through X-ray diffraction or cryo-electron microscopy, the resulting data remains difficult to understand. Thus, molecular simulation tools such as molecular dynamics are … More Computer modelling for fitting possible structures to diffraction data

Understanding the evolutionary dynamics of phosphorylation with fungal species as model system

May 7, 2017

Phosphorylation plays important roles in many aspects of cell biology and intra- and intercellular signaling; for example, serving as markers for epigenetic regulation of gene transcription, and more commonly, as a repository of energy for enzymatic and protein function. But, what determines the selection of specific protein sequence motif as sites for inserting a phosphorus … More Understanding the evolutionary dynamics of phosphorylation with fungal species as model system